Crystal structure of Arginyl-tRNA synthetase

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

Starting Model: experimental
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The crystal structure of arginyl-tRNA synthetase from Homo sapiens

Kim, H.S.Cha, S.Y.Jo, C.H.Han, A.R.Hwang, K.Y.

(2014) FEBS Lett 588: 2328-2334

  • DOI: https://doi.org/10.1016/j.febslet.2014.05.027
  • Primary Citation of Related Structures:  
    4Q2T, 4Q2X, 4Q2Y

  • PubMed Abstract: 

    Arginyl-tRNA synthetase (ArgRS) is a tRNA-binding protein that catalyzes the esterification of L-arginine to its cognate tRNA. L-Canavanine, a structural analog of L-arginine, has recently been studied as an anticancer agent. Here, we determined the crystal structures of the apo, L-arginine-complexed, and L-canavanine-complexed forms of the cytoplasmic free isoform of human ArgRS (hArgRS). Similar interactions were formed upon binding to L-canavanine or L-arginine, but the interaction between Tyr312 and the oxygen of the oxyguanidino group was a little bit different. Detailed conformational changes that occur upon substrate binding were explained. The hArgRS structure was also compared with previously reported homologue structures. The results presented here may provide a basis for the design of new anticancer drugs, such as L-canavanine analogs.

  • Organizational Affiliation

    Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arginine--tRNA ligase, cytoplasmic
A, B
607Homo sapiensMutation(s): 1 
Gene Names: RARS
UniProt & NIH Common Fund Data Resources
Find proteins for P54136 (Homo sapiens)
Explore P54136 
Go to UniProtKB:  P54136
GTEx:  ENSG00000113643 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54136
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.623α = 90
b = 105.234β = 90
c = 172.259γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description